[NetBeans 4.0 FCS, JDK 1.4.2_06]
When I want to change server some properties, I
have to do it when server is running, otherwise
JVMs node are not accessible. But when I change
it, server is not automatically restarted and is
running with old properties. It should be possible
to change properties even with not running server.
Imaging following scenario:
1. Appserver is not running and you want change
debug port. JVMs node is not available, so you
have to start appserver.
2. Change debug port in properties.
3. Stop server.
4. Start server.
You have to do it in 4 steps!

cannot agree more... But this is a constraint from the app server
admin area, not the plugin: to administer the server, icnlduing
changinf debug port, the admin server (which is for PE the same as the
isntance VM) has to be up and running.
For EE enterprise edition, the 2 processes are separate...
Move to RFE.

We need to find a public way to change the properties of a local server without starting that server... and then having
to restart the server to have them take effect. This should be addressed in the v3 plugin... in either 6.5 and/or 7.
If the changes can get into the v2 plugin... without a lot of extra work... all the better.

It is possible to implement offline JVM options editing for local domain but it won't be easy.
There is API in GF that allows to read, modify and store domain.xml file. But it means that GlassFish plugin would have to load some classes from modules and use them to display and modify domain.xml content (servers, configs and jvm-options).
There is no chance to make such a changes in 7.3.